Why would the Alliance have a faction specific ship? The only one would be the Sirius corp (independent) whose Atemis ship or whatever it called was destroyed. This would open up the Sirius Corp branded Ships, which I guess would technically be Alliance.
Core Dynamics have a contract with the Federation, and Gutamaya do with the Empire, which is what is making them 'exclusive' to those factions.
There is plenty of precedent for Alliance specific ships. In Frontier and First Encounters, the Alliance had the largest shipyards in the Galaxy. The main ship in the background plot was also an Alliance ship. They also made capitol ships for the Alliance.
I think he means the 8-sided ones. 
On-topic: I don't see the reasoning for exclusive trade ships. The exclusive ships have military functions. And then there's the issue of what would you base the exclusivity on? There's no Alliance ranking.
Where is it said that exclusive ships 'must' have military functions?
As for no Alliance ranking, well there have been several threadnaughts on the already. Yes, it is something else we want. The Alliance operates a very different system to the other major powers, with individual systems militias coming together to form fleets. So there is no reason you could not have Alliance militia ranks.
People seem to forget the Alliance was forged in war. By kicking both the Federation's and Empire's butts, at the same time, on Alioth.